One of the most important principles of good fictional writing is to put as many obstacles in the protagonist's way as possible. Make them suffer, was the title of an article that appeared in Writer's Digest many years ago.

The obstacles must be hard, but they must be of the kind the protagonistcan overcome. But he is in no way guaranteed that he will overcome them. Often the only way of overcoming the obstacle is through some kind of pain or loss. This creates suspense in the reader (or, of course, viewer when it comes to movies) who wants the protagonist to overcome those obstacles.

In the case of The Matrix, finding a right telephone and getting to it is one of the recurring obstacles. Right at the start, we see Trinity fighting her way out of a building, running to a phone booth, which is then crushed by a big truck. At that point, we do not yet know who she is, whether she is good or bad. We do not know that she got there on time. We do not know why she was running to the booth. All we know is that she is no longer there.

We do remember that opening scene every time anyone is trying to get to the right phone. We now know that it is possible for them to reach the phone (if we did not, we would assume the person looking for the phone was not going to make it). We also know that the agents know our heros need to get to a specific phone and will do everything conceivable to prevent them from getting there (if we did not know that, we would assume the person looking for the phone would get to it without any difficulty). This creates tension and uncertainty, which all good fiction writing is based on (it is actually an excellenttool for non-fiction writers as well, but rarely used in that genre).

Allowing them to use cellularphones would make all this suspense impossible. Sure, Neo could lose his cell phone before the final battle. But that could only happen once. There would be no way to prepare the audience, to build the tension up gradually.

The idea of needing specific phones works. I seriously doubt anyone watching the movie for the first time was thinking why they could not get out of the Matrix on cellular phones. We were all busy thinking, gee, I hope he(she)'ll make it. And, of course, in the final battle we not only wanted Neo to get to the phone, but to get there on time.